SeqCode: buildChIPprofile

General description

Generation of custom tracks of ChIPseq, ATACseq and RNAseq experiments for visualization in genome browsers.

> bin/buildChIPprofile -h

SeqCode_v1.0						User commands						buildChIPprofile

	buildChIPprofile - a program to generate genome-wide ChIPseq/ATACseq/RNAseq profiles for genome browser visualization.

	buildChIPprofile [-c <Rcolor>][-d][-l <bp>][-m][-p][-s <reads>][-w <bp>][-v][-x prefix][-h]
	<chrom_info> <SAM file> <name>

	One folder with one file:
	- BedGraph profile (compressed).

	-c : Track color (default: black).
	-d : Demo mode for small BAM files (min number reads control off).
	-l : Avg. fragment size (default: 150).
	-m : Invert the score of BedGraph records.
	-p : Using pair-end reads mapped in proper pair (default: single-end).
	-s : Number of spike-in reads for reference-adjusted normalization.
	-w : Window resolution (default: 100).
	-v : Verbose. Display info messages.
	-x : Prefix for the output folder.
	-h : Show this help.

	SeqCode homepage:
	GitHub source code:

	Written by Enrique Blanco.

SeqCode_v1.0						User commands						buildChIPprofile


Example 1: Generate the custom track of the ChIPseq experiment to be visualized in the UCSC genome browser.

> bin/buildChIPprofile -v ChromInfo.txt SRR1015741.bam H3K4me3

Example 2. Generate in higher resolution the custom track of the same ChIPseq sample.

> bin/buildChIPprofile -v -w 10 ChromInfo.txt SRR1015741.bam H3K4me3_w10

Example 3: Generate the custom tracks of the strand-specific RNAseq experiment.

> bin/buildChIPprofile -v ChromInfo.txt SRR1699465/accepted_hits_plus.bam RNAseq+
> bin/buildChIPprofile -mv ChromInfo.txt SRR1699465/accepted_hits_minus.bam RNAseq-

ChIPseq and RNAseq samples

Please, follow the link below for further information on how to get and preprocess the raw data of published ChIPseq and RNAseq samples utilized in this glossary of SeqCode functions.